Protein substructures and folded stability

Protein substructures detected in proton-exchange experiments can be described in quantitative detail with the Debye-Waller temperature factors from diffraction studies. The smallest substructures, in mesophilic proteins approximately 12% of the total residues, determine thermodynamic as well as kinetic stability by electrostatic synergism of a few tightly packed clusters about central peptide-peptide hydrogen bonds. Fixed positions of the clusters establish genetic stability of a protein family. The normal product of thermal denaturation above 280 K in dilute buffers, a compact but motile bubble, is formed with positive free-energy change in step from native state the single transition state and smaller negative change in the step from transition state to product. The largest substructures, approximately 80% of the residues, undergo changes in atom free volumes in function that are small relative to coordinate errors in protein diffraction studies but nevertheless describe the most important conformation changes. The criterion of precision in protein construction is approximately 0.05 A and may be found to be smaller when precision in X-ray diffraction improves. The ratio of residues in the two substructures is fixed in mesophiles.